Moments before the meeting, Premier Doug Ford blamed the federal government's immigration policies for putting a strain on local and provincial resources, saying Trudeau's administration has encouraged people to cross into Canada illegally.
"If he wants to welcome them in, that's fine, but he should make sure he's paying for them and compensating the municipalities as well as the provincial government".
Trudeau met with Doug Ford in Toronto this afternoon, and said afterwards he spent some time explaining to the premier how the asylum-seeking system works.
With the federal government paying a fraction of the cost of resettling migrants and Ontario now backing away from an earlier commitment made by the former Liberal government, cities in the province are anxious about who will pay for overtaxed public services and shelters.
"This has resulted in a housing crisis and threats to the services that Ontario families depend on", Ford's office said in the statement.
"To those fleeing persecution, terror & war, Canadians will welcome you, regardless of your faith".
Prime Minister Justin Trudeau is suggesting Ontario's new premier doesn't fully understand Canada's worldwide obligations when it comes to dealing with refugee claimants.
"Thousands of refugee claimants and asylum seekers are in Toronto's shelter system - this includes 800 people, many who are children, who will need shelter after August 9 when we can no longer use two college dormitories", Tory said in a statement Thursday.
Verbal sparring aside, it's unclear what the Ford government's declaration could mean for Ontario municipalities - especially Toronto - that are already struggling to accommodate an influx of asylum seekers.
It comes as the province's Attorney-General, Caroline Mulroney, says in a letter to Toronto Mayor John Tory that the federal bail system is allowing "too many violent criminals back into our streets", and follows the cancellation of the provincial cap-and-trade program for pricing carbon.
Mr. Tory said he was speaking regularly to federal Immigration Minister Ahmed Hussen and that he would urge Ottawa to take immediate action.
The Ontario government says Ottawa is to blame for a housing crisis caused by people crossing the border illegally and should pay all the costs.
"The premier and I talked directly about the fact that we have very clear mandates from the people who elected us", he said.
Toronto is now dealing with a crisis as Mayor John Tory asked for help last week as his city is overwhelmed with waves of refugees and asylum seekers.
The feds have also directed $11 million to Ontario to help with the additional costs related to what they term irregular migration.
Now, it's unclear whether the new triage system can proceed without the provincial government's participation. "The downstream effects of not having a triage system in place are going to be very hard for the municipalities".
With more than 3,000 refugees in Toronto, the federal government will now organize the data collection and response to the asylum issue that the province had committed to past year.
While the province has now made its position clear, Tory said in his statement, he's hoping the federal government will "fulfil its responsibility to help cities deal with these families".
Tory said the city has exhausted the resources, personnel and available spaces it needs to house refugees, and needs help. "In the last number of months, the numbers have been dropping, and the numbers are promising". "This can not continue and must be resolved".